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(-) Description

Title :  PANTOTHENATE SYNTHETASE IN COMPLEX WITH N,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE
 
Authors :  A. Ciulli, H. L. Silvestre, T. L. Blundell, C. Abell
Date :  29 Mar 12  (Deposition) - 13 Mar 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Alpha Beta/3-Layer Sandwich/Rossmann Fold, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Silvestre, T. L. Blundell, C. Abell, A. Ciulli
Integrated Biophysical Approach To Fragment Screening And Validation For Fragment-Based Lead Discovery.
Proc. Natl. Acad. Sci. Usa V. 110 12984 2013
PubMed-ID: 23872845  |  Reference-DOI: 10.1073/PNAS.1304045110

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-300
    Gene: MT3707, MTCY07H7B.20, PANC, RV3602C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: PS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
10OC3Ligand/IonN,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE
2EOH7Ligand/IonETHANOL
3GOL3Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 15)
No.NameCountTypeFull Name
10OC3Ligand/IonN,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE
2EOH7Ligand/IonETHANOL
3GOL3Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
10OC1Ligand/IonN,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE
2EOH4Ligand/IonETHANOL
3GOL2Ligand/IonGLYCEROL
4IMD-1Ligand/IonIMIDAZOLE
5SO41Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:38 , THR A:39 , MET A:40 , PHE A:67 , ASN A:69 , VAL A:142 , VAL A:143 , LEU A:146 , PHE A:157 , GLN A:164 , HOH A:506BINDING SITE FOR RESIDUE 0OC A 401
02AC2SOFTWAREPRO A:70 , GLN A:72BINDING SITE FOR RESIDUE 0OC A 402
03AC3SOFTWAREMET A:109 , TYR A:110 , PRO A:111 , ASP A:112 , GLY A:113 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWARELEU A:114 , ARG A:115 , THR A:117 , GLN B:119 , PRO B:120 , HOH B:675BINDING SITE FOR RESIDUE EOH A 404
05AC5SOFTWARETHR A:218 , HIS B:222 , THR B:225BINDING SITE FOR RESIDUE EOH A 405
06AC6SOFTWAREPRO A:70 , GLN A:72BINDING SITE FOR RESIDUE IMD A 406
07AC7SOFTWARESER A:24 , ARG A:28 , VAL A:150 , ARG A:151BINDING SITE FOR RESIDUE EOH A 407
08AC8SOFTWAREPRO B:38 , THR B:39 , PHE B:67 , ASN B:69 , VAL B:142 , VAL B:143 , LEU B:146 , GLN B:164 , EOH B:406 , HOH B:520BINDING SITE FOR RESIDUE 0OC B 401
09AC9SOFTWAREGLY B:244 , ARG B:273 , GLY B:275BINDING SITE FOR RESIDUE GOL B 402
10BC1SOFTWAREHIS B:44 , HIS B:47 , ASP B:161BINDING SITE FOR RESIDUE SO4 B 403
11BC2SOFTWAREASP A:178 , ALA B:21 , SER B:24 , ARG B:25 , GLN B:148 , ILE B:149 , VAL B:150 , ARG B:151 , HOH B:597BINDING SITE FOR RESIDUE GOL B 404
12BC3SOFTWARETHR B:39 , MET B:40 , HIS B:47 , 0OC B:401 , HOH B:687 , HOH B:705BINDING SITE FOR RESIDUE EOH B 406
13BC4SOFTWAREGLN B:206 , GLY B:275 , THR B:276 , HOH B:566BINDING SITE FOR RESIDUE EOH B 407
14BC5SOFTWAREARG B:253 , LEU B:257 , GLY B:258 , PRO B:259BINDING SITE FOR RESIDUE EOH B 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EFK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:289 -Phe A:290
2Ala A:291 -Gly A:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EFK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EFK)

(-) Exons   (0, 0)

(no "Exon" information available for 4EFK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4efka_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhh...eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeeeeeee.........eeeeeeeeee..eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4efk A   4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPLNGSGRLLVAARLGTTRLLDNIAIEIGTFAG 292
                                    13        23        33        43        53        63        73|       90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       262       272       282       292
                                                                                                73|                                                                                                                                                                               259|                              
                                                                                                 81                                                                                                                                                                                262                              


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4efkb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4efk B   1 MAIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    10        20        30        40        50        60        70|       94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
                                                                                                70|                                                                                                                                                                                                           
                                                                                                 85
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EFK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EFK)

(-) Gene Ontology  (13, 20)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PANC_MYCTO | P9WIL4: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a7x 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4fzj 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun
        PANC_MYCTU | P9WIL5: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a7x 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4fzj 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun

(-) Related Entries Specified in the PDB File

3ime 4ddh 4ddk 4ddm 4de5 4ef6